9KBO

Crystal structure of human Shiftless (SFL) containing phosphorylation sites Ser249, Thr250, Thr253 and Ser256

Summary for 9KBO

• Entry DOI: 10.2210/pdb9kbo/pdb
• Descriptor: Shiftless antiviral inhibitor of ribosomal frameshifting protein, ZINC ION (3 entities in total)
• Functional Keywords: host factor, antivirus, -1 prf, rna-bingding, antiviral protein
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 4
• Total formula weight: 134371.88

Authors

Zhang, Y.,Li, Z.,Chong, H.,Hou, P.,Hao, W.,Li, M.,Liu, Z.,Jia, W.,Qin, B.,He, Y.,Cui, S. (deposition date: 2024-10-31, release date: 2025-11-19, Last modification date: 2025-12-31)

Primary citation

Zhang, Y.,Li, Z.,Chong, H.,Hou, P.,Hao, W.,Li, M.,Liu, Z.,Jia, W.,Qin, B.,He, Y.,Cui, S.
Phosphorylation of shiftless is important for inhibiting the programmed -1 ribosomal frameshift.
Sci Adv, 11:eadw7471-eadw7471, 2025

PubMed Abstract: Shiftless (SFL) is a broad-spectrum inhibitor of programmed -1 ribosomal frameshift (-1 PRF) and exhibits various antiviral activities. Here, we characterized human SFL structurally and biochemically. The 2.0-angstrom resolution crystal structure of SFL reveals a boat-like module comprising an N-terminal helical bundle and three zinc fingers at the C terminus. A hyperphosphorylation loop (HPL) buried between the helical bundle and the zinc finger 1 harbors four phosphorylated residues (p-S249, p-T250 p-T253, and p-S256), which are important to protein folding. SFL forms monomers in solution and binds the HIV-1 -1 PRF sequence with nanomolar affinity ( = 5.7 nanomolar). Disruption of HPL phosphorylation decreased the RNA binding affinity and undermined the SFL-mediated -1 PRF inhibition of various viruses. Proximity-dependent biotinylation identified three cellular Ser/Thr kinases-EEF2K, NEK9, and PBK-that phosphorylate SFL in cells. These findings shed light on the mechanisms underlying -1 PRF regulation by SFL and provide insights into the role of SFL in virus inhibition.

PubMed: 41417896
DOI: 10.1126/sciadv.adw7471

Experimental method

X-RAY DIFFRACTION (2 Å)